Btw, I forgot: plyr_1.7.1 is also required for package_gatk_1_4. Hence
the install_url call for it below.
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Thu, Jul 31, 2014 at 1:51 PM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
> Hi Evan,
>
> unfortunately I have no access to this repository. I'm only the maintainer
> of the galaxytools in github. But I have CC'ed Dave, he is responsible for
> the devteam packages!
>
> Cheers and thanks for sharing your information!
> Bjoern
>
> Am 31.07.2014 um 20:47 schrieb Evan Bollig:
>
>> Bjoern,
>>
>> FYI, I found that package_gatk_1_4 from the main Galaxy toolshed
>> produces Rscript files for VariantRecalibrator and other commands that
>> require ggplot_0.8.8 and reshape_0.8.4. This applies to GATK versions
>> 1.4-20 and 1.4-37.
>>
>> The magic incantation to get a systemwide R v3.1 setup properly is:
>>
>> r <- getOption("repos");
>> r["CRAN"] <- "http://cran.rstudio.com/";;
>> options(repos=r);
>> install.packages(c('devtools','gsalib'));
>> require(devtools);
>>
>> install_url('http://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.7.1.tar.gz');
>>
>> install_url('http://cran.r-project.org/src/contrib/Archive/reshape/reshape_0.8.4.tar.gz');
>>
>> install_url('http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.8.8.tar.gz');
>>
>> I'm not sure gsalib is required, but it is better to play it safe IMO.
>>
>> Can you add this to the package_gatk_1_4 documentation to help others
>> along? It would be even better if the package_gatk_1_4 could also
>> install those R libraries itself.
>>
>> Cheers,
>>
>> -E
>> -Evan Bollig
>> Research Associate | Application Developer | User Support Consultant
>> Minnesota Supercomputing Institute
>> 599 Walter Library
>> 612 624 1447
>> e...@msi.umn.edu
>> boll0...@umn.edu
>>
>>
>> On Tue, Jul 29, 2014 at 4:22 PM, Björn Grüning
>> <bjoern.gruen...@gmail.com> wrote:
>>>
>>>
>>>
>>> Am 29.07.2014 um 22:45 schrieb Evan Bollig:
>>>
>>>> Hey Bjoern,
>>>>
>>>> I'm trying to use variant_recalibrator, xy_plot and other tools that
>>>> depend on package_r_2_11_0 and require ggplot2 to be installed. Since
>>>> CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a
>>>> better idea to update the packages the depend on those versions to R
>>>> 3.0 or 3.1?
>>>
>>>
>>>
>>> Yes, this would be a better idea!
>>>
>>>
>>>> The variant_recalibrator tool generates an Rscript
>>>> incompatible with modern versions of ggplot2, so this could be a quite
>>>> involved undertaking.
>>>
>>>
>>>
>>> Oh :( ... can we somehow get an old tarball of ggplot2? Have you looked
>>> at
>>> older linux disributions, debian stable for example?
>>>
>>> I found ggplot on download_store ;)
>>>
>>> https://github.com/bgruening/download_store/blob/master/gatk2_R_deps/ggplot2_0.9.3.1.tar.gz
>>>
>>> Is that old enough?
>>>
>>>
>>>> Meanwhile I'll look into the download_store option. You download all
>>>> of the tarballs and install them individually with R CMD INSTALL?
>>>
>>>
>>>
>>> Not really, we have a nice routine in the toolshed for such tasks:
>>> Have a look at:
>>>
>>> https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_deseq2_1_2_10
>>>
>>> Note: the order of the packages are important ...
>>>
>>> Ciao,
>>> Bjoern
>>>
>>>
>>>> Cheers,
>>>>
>>>> -E
>>>> -Evan Bollig
>>>> Research Associate | Application Developer | User Support Consultant
>>>> Minnesota Supercomputing Institute
>>>> 599 Walter Library
>>>> 612 624 1447
>>>> e...@msi.umn.edu
>>>> boll0...@umn.edu
>>>>
>>>>
>>>> On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning
>>>> <bjoern.gruen...@gmail.com> wrote:
>>>>>
>>>>>
>>>>> Hi Evan,
>>>>>
>>>>> do you have somehow access to this tarball? Than we can put it on
>>>>>
>>>>> https://github.com/bgruening/download_store
>>>>>
>>>>> I use that to host R packages to save them for reproducibility.
>>>>>
>>>>>
>>>>>> Can I install another package_r and have packages that depend on
>>>>>> package_r_2_11_0 use the newer version?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> I don't think so. But that depends very much on your package. Is it not
>>>>> possible to use a newer R version? In either case you should save all
>>>>> tarballs somehow to archive them!
>>>>>
>>>>> Cheers,
>>>>> Bjoern
>>>>>
>>>>>> -Evan Bollig
>>>>>> Research Associate | Application Developer | User Support Consultant
>>>>>> Minnesota Supercomputing Institute
>>>>>> 599 Walter Library
>>>>>> 612 624 1447
>>>>>> e...@msi.umn.edu
>>>>>> boll0...@umn.edu
>>>>>> ___________________________________________________________
>>>>>> Please keep all replies on the list by using "reply all"
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>>>>>>
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>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>>
>>>>>
>>>
>
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